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Adedeji Olulana AF, Choi D, Inverso V, Redhu SK, Vidonis M, Crevatin L, Nicholson AW, Castronovo M. Noncanonical DNA Cleavage by BamHI Endonuclease in Laterally Confined DNA Monolayers Is a Step Function of DNA Density and Sequence. Molecules 2022; 27:5262. [PMID: 36014501 PMCID: PMC9416302 DOI: 10.3390/molecules27165262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Cleavage of DNA at noncanonical recognition sequences by restriction endonucleases (star activity) in bulk solution can be promoted by global experimental parameters, including enzyme or substrate concentration, temperature, pH, or buffer composition. To study the effect of nanoscale confinement on the noncanonical behaviour of BamHI, which cleaves a single unique sequence of 6 bp, we used AFM nanografting to generate laterally confined DNA monolayers (LCDM) at different densities, either in the form of small patches, several microns in width, or complete monolayers of thiol-modified DNA on a gold surface. We focused on two 44-bp DNAs, each containing a noncanonical BamHI site differing by 2 bp from the cognate recognition sequence. Topographic AFM imaging was used to monitor end-point reactions by measuring the decrease in the LCDM height with respect to the surrounding reference surface. At low DNA densities, BamHI efficiently cleaves only its cognate sequence while at intermediate DNA densities, noncanonical sequence cleavage occurs, and can be controlled in a stepwise (on/off) fashion by varying the DNA density and restriction site sequence. This study shows that endonuclease action on noncanonical sites in confined nanoarchitectures can be modulated by varying local physical parameters, independent of global chemical parameters.
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Affiliation(s)
- Abimbola F. Adedeji Olulana
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Regional Centre for Rare Diseases, University Hospital Udine, 33100 Udine, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Dianne Choi
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Vincent Inverso
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Marco Vidonis
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Department of Chemistry, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Luca Crevatin
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Allen W. Nicholson
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Matteo Castronovo
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Regional Centre for Rare Diseases, University Hospital Udine, 33100 Udine, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
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